The Flame malware was distributed using a fake certificate that was generated via a brand new (publicly unknown) chosen prefix collision technique against SHA-1.
Microsoft is providing an update for all supported releases of Microsoft Windows. The update revokes the trust of the following intermediate CA certificates:
Microsoft Enforced Licensing Intermediate PCA (2 certificates)
Microsoft Enforced Licensing Registration Authority CA (SHA1)
(from http://technet.microsoft.com/en-us/security/advisory/2718704)Two of the certs were MD5, the third was SHA1.
SHA-3 is the product of a peer-reviewed cryptographic contest.
That should be reason enough not to use SHA.
While SHA-1 should not be trusted too much because it has shown possible theoretical attacks SHA-2 still holds. Also these kind of things are IP - there are a lot of eyeballs and scrutiny going on.
There is much bigger chance of fraked up implementation that will make it insecure than the theory - there are a lot of independent researchers that have scrutinized them quite a bit. And while I am sure NSA employs a lot of very capable people they do not hold monopoly on world class cryptographers.